Resource
| Id | TF_ChIP-seq/ENCSR000BGD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BGD [biosample_summary="Homo sapiens GM12878" and target="POLR2A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN442QXS|/analyses/ENCAN442QXS/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF865BUP|/files/ENCFF865BUP/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19981239 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting POLR2A-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF865BUP|/files/ENCFF865BUP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF591BQK|/files/ENCFF591BQK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGD | float |
TF_ChIP-seq_ENCSR000BGD |
TF_ChIP-seq ENCSR000BGD [biosample_summary="Homo sapiens GM12878" and target="POLR2A"]
|
 |
[5.58, 533] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 20981817 | 0.65% | 44448 |
| chr1 | 1902066 | 0.76% | 4005 |
| chr2 | 1273005 | 0.53% | 2633 |
| chr3 | 1009690 | 0.51% | 2030 |
| chr4 | 605896 | 0.32% | 1262 |
| chr5 | 862015 | 0.47% | 1775 |
| chr6 | 1080925 | 0.63% | 2125 |
| chr7 | 949628 | 0.60% | 2046 |
| chr8 | 678332 | 0.47% | 1440 |
| chr9 | 887676 | 0.64% | 1955 |
| chr10 | 752666 | 0.56% | 1578 |
| chr11 | 1171935 | 0.87% | 2461 |
| chr12 | 1030376 | 0.77% | 2196 |
| chr13 | 336147 | 0.29% | 709 |
| chr14 | 702248 | 0.66% | 1471 |
| chr15 | 673048 | 0.66% | 1416 |
| chr16 | 1180586 | 1.31% | 2661 |
| chr17 | 1513114 | 1.82% | 3178 |
| chr18 | 289590 | 0.36% | 602 |
| chr19 | 1955420 | 3.34% | 4264 |
| chr20 | 666350 | 1.03% | 1420 |
| chr21 | 286831 | 0.61% | 619 |
| chr22 | 719226 | 1.42% | 1617 |
| chrX | 455047 | 0.29% | 985 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44448 | 1 | 9967 | 472.05 | 402 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF120VUT.bed.gz | 800.86 KB | bca31e848a128f562b9082c678c3ad04 |
| ENCFF120VUT.tabix.bed.gz | 518.95 KB | 09a74248e52b48891830cc7992bff648 |
| ENCFF120VUT.tabix.bed.gz.tbi | 144.09 KB | 28cedbbc3af8b5240d956dd4035639b5 |
| genomic_resource.yaml | 3.39 KB | 66ba998e9e7f0ad319854ae76100864e |
| statistics/ |